plot_st_cor_heatmap: Plot heatpmap of correlation between marker genes and cell...

In ZJUFanLab/SpaTalk: Infer Cell-Cell Communication for Spatial Transcriptomics

Plot heatpmap of correlation between marker genes and cell types

Description

Plot heatpmap of correlation between the expression of marker genes and the predicted score of cell types among all spatial cells or spots.

Usage

plot_st_cor_heatmap(
  object,
  marker_genes,
  celltypes,
  color_low = NULL,
  color_mid = NULL,
  color_high = NULL,
  scale = "none",
  if_show_top = T,
  top_direction = "row",
  border_color = NA
)

Arguments

object	SpaTalk object generated from dec_celltype.
marker_genes	A character containing the known marker genes to plot, provide at least two marker genes of interest.
celltypes	A character containing name of cell type in the sc_celltype. Default is to plot all cell types.
color_low	Color for the lowest value.
color_mid	Color for the middle value for using scale_color_gradient2. Default is NULL.
color_high	Color for the highest value.
scale	Character indicating if the values should be centered and scaled in either the row direction or the column direction, or none. Corresponding values are 'row', 'column' and 'none'.
if_show_top	Whether to plot a symbol to the highest value across rows or columns. Default is TRUE.
top_direction	Direction to identify the highest value, select 'row' or 'column'.
border_color	Color of the cell border. Default is 'NA'.

ZJUFanLab/SpaTalk documentation built on Jan. 21, 2025, 3:13 p.m.